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H3N2 aptamer
Description
In 2006, Kumar, P. K. R et al. used the SELEX method to select the aptamer binds specifically to the haemagglutinin (HA) region of the target strain A/Panama/2007/1999 (H3N2) and failed to recognize other human influenza viruses, including another strain with the same subtype, H3N2. This study demonstrates the potential application of aptamers in influenza virus genotyping and functional research, and may be helpful for developing new antiviral strategies[1].
SELEX
In 2006, Kumar, P. K. R et al. derived aptamers from a random RNA sequence library via the SELEX technique. From the tenth screening round, 17 clones were sequenced and their sequences categorised into three main groups. They also employed surface plasmon resonance (SPR) to pinpoint the phosphate groups in the ligand vital for HA binding, and mapped the smallest RNA motif capable of binding to the A/Panama virus HA[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw. P30-10-16 apatamer binds to haemagglutinin (HA) region of the target strain A/Panama/2007/1999 (H3N2). P30-10-16 apatamer was named by Kumar, P. K. R et al[1].
5'-GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU-3'
Ligand information
SELEX ligand
Some isolated sequences bind to the affinity of the protein[1].
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| P30-10-16 | 5'-GGGAGAAUUCCGACCAGAAGGGUUAAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU-3' | Haemagglutinin (HA) region of the target strain A/Panama/2007/1999 (H3N2) | 188 pM |
Structure ligand
Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization either through clathrin-dependent endocytosis or through clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.-----From Uniprot
UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.
Pfam: a widely recognised database of protein families and domains.
GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.
Mass: an intrinsic property of a body.
| Name | Uniprot ID | Pfam | Mass | Protein sequence | PDB ID | GenBank |
|---|---|---|---|---|---|---|
| Haemagglutinin (HA) region of the target strain A/Panama/2007/1999 (H3N2) | A0A097PF13 | IPR000149 | 63.635 kDa |
......
MKTIIALSYILCLVFAQKLPGNDNSTATLCLGHHAVSNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILDGENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLNYKYPALNVTMPNNEKFDKLYIWGVLHPSTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQINGKLNRLIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI
|
NA | AY832929.1 |
References
[1] An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion.Gopinath, S. C. B., Misono, T. S., Kawasaki, K., Mizuno, T., Imai, M., Odagiri, T., & Kumar, P. K. R.
The Journal of general virology, 87(Pt 3), 479–487. (2006)